| 1 | |
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| 2 | Welcome to the ARB Sequence Analysis Suite |
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| 3 | |
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| 4 | |
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| 5 | System Requirements |
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| 6 | ------------------- |
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| 7 | |
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| 8 | Operating System: Linux or OSX |
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| 9 | Harddrive: 200 MB for arb (+some GB for databases) |
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| 10 | Memory: much |
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| 11 | |
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| 12 | Notes: |
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| 13 | |
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| 14 | The resources required for ARB to run smoothly depend on the |
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| 15 | size of the database(s) you intend to work with. Large |
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| 16 | databases, especially the SSU databases provided by the |
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| 17 | SILVA project, require large amounts of fast memory. |
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| 18 | |
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| 19 | Please refer to http://bugs.arb-home.de/wiki/SystemRequirements |
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| 20 | for details on memory usage. |
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| 21 | |
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| 22 | |
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| 23 | Choose ARB version: |
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| 24 | ------------------- |
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| 25 | |
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| 26 | Currently there are two arb versions available: |
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| 27 | * the frequently updated PRODUCTION version (recommended) |
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| 28 | * the last stable public RELEASE version |
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| 29 | |
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| 30 | |
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| 31 | Installation using Package Managers: |
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| 32 | ---------------------------------- |
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| 33 | |
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| 34 | OSX: |
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| 35 | |
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| 36 | Please refer to |
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| 37 | https://github.com/arb-project/homebrew-arb |
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| 38 | |
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| 39 | Linux: |
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| 40 | |
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| 41 | We generally recommend installation from Pre-Compiled Binary (see below)! |
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| 42 | |
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| 43 | Some arb versions are distributed via apt or launchpad. |
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| 44 | These versions are modified (to fit better into linux systems), |
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| 45 | but they are not supported nor tested by us. |
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| 46 | |
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| 47 | |
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| 48 | Installation from Pre-Compiled Binaries: |
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| 49 | ---------------------------------------- |
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| 50 | |
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| 51 | 1) Download "arb_install.sh" and the arb-*.tgz matching your distribution |
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| 52 | |
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| 53 | * for production version from http://download.arb-home.de/production/latest/ |
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| 54 | * for release version from http://download.arb-home.de/release/latest/ |
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| 55 | |
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| 56 | We currently only provide a few precompiled versions: |
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| 57 | |
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| 58 | arb-*.debian#-amd64.tgz |
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| 59 | arb-*.ubuntu#-amd64.tgz |
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| 60 | |
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| 61 | (here '*' stands for the version or revision number, e.g. '6.0.6' or 'r17491' |
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| 62 | and '#' stands for the OS version number) |
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| 63 | |
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| 64 | Note: |
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| 65 | * all versions are compiled without OPENGL |
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| 66 | |
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| 67 | 2) Install using "arb_install.sh" |
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| 68 | |
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| 69 | Open a terminal, change to the directory where you have saved the |
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| 70 | files needed for installation: |
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| 71 | |
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| 72 | 'arb_install.sh' // install script |
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| 73 | 'arb_README.txt' // this file |
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| 74 | 'arb-*.tgz' // your chosen ARB version |
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| 75 | |
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| 76 | and type |
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| 77 | |
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| 78 | bash arb_install.sh |
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| 79 | |
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| 80 | (to install arb for all users call the script as root or via sudo) |
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| 81 | |
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| 82 | Answer all questions asked by the script. |
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| 83 | |
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| 84 | Notes: |
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| 85 | - The script will ask about a pt_server directory. This is a |
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| 86 | directory where arb will store big index files. |
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| 87 | You should enter a different path as you do not want to |
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| 88 | recreate those files after an ARB update. |
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| 89 | - Normally pressing enter will be a good choice. |
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| 90 | - You can rerun the script as often as needed. |
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| 91 | It can be used to reconfigure an existing arb installation. |
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| 92 | |
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| 93 | Change your ".cshrc" or ".profile" files or create an 'arb' alias. |
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| 94 | |
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| 95 | To do so, follow the instructions printed when installation |
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| 96 | does succeed. |
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| 97 | |
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| 98 | 3) Install library dependencies. |
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| 99 | |
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| 100 | ARB needs: |
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| 101 | gnuplot, gv, openmotif, xfig, transfig, xterm, libtiff, libX11, libXaw, |
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| 102 | libXext, libxml2, libXpm, libXt, lynx, time, libxslt, glib2, readline |
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| 103 | |
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| 104 | On Centos, dependencies should be satisfied by running: |
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| 105 | |
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| 106 | sudo yum install gnuplot openmotif xfig transfig xterm libXpm \ |
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| 107 | libtiff libX11 libXaw libXext libxml2 libXpml libXt lynx \ |
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| 108 | time libxslt readline glib2 |
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| 109 | |
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| 110 | On Ubuntu use the package installation script delivered together with arb: |
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| 111 | |
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| 112 | SH/arb_installubuntu4arb.sh |
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| 113 | |
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| 114 | If any of the packages is not available on your system, it might just |
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| 115 | have a slightly differing name. Try using "yum search" or |
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| 116 | "apt-cache search" to search for packages matching the base name |
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| 117 | (e.g. "yum search libxpm") and pick the one that's available. The only |
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| 118 | known issue is that you must not use "lesstif" instead of |
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| 119 | motif/openmotif (if you do, the GUI will be corrupted). |
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| 120 | |
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| 121 | 4) prepare alias / PATH for arb |
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| 122 | |
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| 123 | During step 2) above, the script should have advised you howto |
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| 124 | change your login script or howto create an alias. |
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| 125 | |
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| 126 | Then go to a directory with a demo database (e.g. 'demo.arb' in the |
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| 127 | arb installation directory) and start 'ARB' by typing |
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| 128 | |
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| 129 | arb |
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| 130 | |
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| 131 | |
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| 132 | Alternatively: |
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| 133 | |
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| 134 | You can now run ARB simply by entering "./bin/arb" from the folder |
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| 135 | where you installed ARB into. For convenience, put a symlink to |
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| 136 | that file into any folder that is in your PATH so that you can |
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| 137 | just type "arb" to run it. |
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| 138 | |
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| 139 | |
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| 140 | 5) install some more fonts |
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| 141 | |
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| 142 | apt-get install \ |
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| 143 | x11-xfs-utils gsfonts-x11 \ |
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| 144 | xfonts-terminus xfonts-terminus-dos xfonts-terminus-oblique |
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| 145 | |
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| 146 | |
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| 147 | Compiling ARB from source |
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| 148 | ------------------------- |
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| 149 | |
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| 150 | * See arb_INSTALL.txt for information about how to compile |
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| 151 | arb from source. |
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| 152 | |
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| 153 | |
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| 154 | Additional information |
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| 155 | ---------------------- |
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| 156 | |
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| 157 | * See arb_INSTALL.txt for additional software needed and/or useful |
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| 158 | together with ARB. |
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| 159 | |
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| 160 | |
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| 161 | PT_server |
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| 162 | --------- |
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| 163 | |
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| 164 | To Install 'ARB' you have to know that some modules use a so |
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| 165 | called 'pt_server' (prefix tree server). |
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| 166 | |
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| 167 | ARB needs a writeable directory to store the pt_server files. |
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| 168 | Those files are needed for fast database search |
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| 169 | (by probe_design, probe_match and the automatic aligner) |
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| 170 | and need a lot of disc space (up to several 100 mega bytes, |
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| 171 | e.g. 4000 16S RNA sequences require about 40 MB). |
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| 172 | This files are not created now. They can be build by any user via |
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| 173 | <ARB_NTREE/Probes/PT_SERVER admin/Build server> |
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| 174 | You may define a special directory as the pt_server files location. |
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| 175 | This prevents any loss of data installing a new version of |
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| 176 | ARB. |
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| 177 | To minimize the use of resources in a workstation cluster |
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| 178 | only one pt_server for each database is started on a user defined |
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| 179 | host. The first user starts the pt_server, and all other users |
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| 180 | can connect to it. |
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| 181 | |
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| 182 | |
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| 183 | The Database |
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| 184 | ------------ |
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| 185 | |
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| 186 | In the current release a small dataset (demo.arb) is provided. |
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| 187 | This database contains a selection of artificial and real-life |
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| 188 | sequences. |
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| 189 | |
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| 190 | The intention of providing this small dataset first is to give |
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| 191 | you the opportunity to get familiar with the program and to |
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| 192 | test the performance of your computer system as well as the |
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| 193 | stability of ARB on your system. |
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| 194 | |
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| 195 | |
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| 196 | Bugs |
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| 197 | ---- |
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| 198 | |
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| 199 | ARB is running properly and stably on our systems. However, it |
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| 200 | may be that there are bugs never detected by us or never |
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| 201 | appearing on our systems. Please don't hesitate to inform us |
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| 202 | about any bugs. A detailed description of the steps performed |
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| 203 | before the problem was evident and of the number and types of |
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| 204 | modules running at the same time would be extremely helpful to |
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| 205 | our computer scientists. |
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| 206 | |
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| 207 | Please report bugs into our bug tracker at |
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| 208 | http://bugs.arb-home.de/ |
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| 209 | |
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| 210 | |
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| 211 | Support |
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| 212 | ------- |
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| 213 | |
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| 214 | Please send any comments, bug reports or questions to |
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| 215 | |
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| 216 | arb@arb-home.de |
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| 217 | |
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| 218 | |
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| 219 | Copyright Notice |
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| 220 | ---------------- |
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| 221 | |
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| 222 | Please see the file |
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| 223 | |
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| 224 | arb_LICENSE.txt |
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| 225 | |
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| 226 | in the ARB installation directory. |
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| 227 | |
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| 228 | |
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| 229 | Disclaimer |
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| 230 | ---------- |
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| 231 | |
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| 232 | THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED |
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| 233 | FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT |
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| 234 | NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF |
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| 235 | FITNESS FOR A PARTICULAR PURPOSE. |
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| 236 | |
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| 237 | |
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| 238 | Have fun! |
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| 239 | |
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